First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan

ABSTRACTWastewater-based epidemiology is a powerful tool to understand the actual incidence of coronavirus disease 2019 (COVID-19) in a community because severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, can be shed in the feces of infected individuals regardless of their symptoms. The present study aimed to assess the presence of SARS-CoV-2 RNA in wastewater and river water in Yamanashi Prefecture, Japan, using four quantitative and two nested PCR assays. Influent and secondary-treated (before chlorination) wastewater samples and river water samples were collected five times from a wastewater treatment plant and three times from a river, respectively, between March 17 and May 7, 2020. The wastewater and river water samples (200–5,000 mL) were processed by using two different methods: the electronegative membrane-vortex (EMV) method and the membrane adsorption-direct RNA extraction method. Based on the observed concentrations of indigenous pepper mild mottle virus RNA, the EMV method was found superior to the membrane adsorption-direct RNA extraction method. SARS-CoV-2 RNA was successfully detected in one of five secondary-treated wastewater samples with a concentration of 2.4 × 103 copies/L by N_Sarbeco qPCR assay following the EMV method, whereas all the influent samples were tested negative for SARS-CoV-2 RNA. This result could be attributed to higher limit of detection for influent (4.0 × 103–8.2 × 104 copies/L) with a lower filtration volume (200 mL) compared to that for secondary-treated wastewater (1.4 × 102–2.5 × 103 copies/L) with a higher filtration volume of 5,000 mL. None of the river water samples tested positive for SARS-CoV-2 RNA. Comparison with the reported COVID-19 cases in Yamanashi Prefecture showed that SARS-CoV-2 RNA was detected in the secondary-treated wastewater sample when the cases peaked in the community. This is the first study reporting the detection of SARS-CoV-2 RNA in wastewater in Japan.

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Identification of Human and Animal Adenoviruses and Polyomaviruses for Determination of Sources of Fecal Contamination in the Environment

Applied and Environmental Microbiology ◽

10.1128/aem.01090-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7886-7893 ◽

Cited By ~ 114

Author(s):

Ayalkibet Hundesa ◽

Carlos Maluquer de Motes ◽

Silvia Bofill-Mas ◽

Nestor Albinana-Gimenez ◽

Rosina Girones

Keyword(s):

River Water ◽

Water Samples ◽

Environmental Samples ◽

Fecal Contamination ◽

Source Tracking ◽

Animal Origin ◽

Urban Sewage ◽

River Water Samples ◽

Negative Results ◽

Wastewater Samples

ABSTRACT The Adenoviridae and Polyomaviridae families comprise a wide diversity of viruses which may be excreted for long periods in feces or urine. In this study, a preliminary analysis of the prevalence in the environment and the potential usefulness as source-tracking tools of human and animal adenoviruses and polyomaviruses has been developed. Molecular assays based on PCR specifically targeting human adenoviruses (HAdV), porcine adenoviruses (PAdV), bovine adenoviruses (BAdV), and bovine polyomaviruses (BPyV) were applied to environmental samples including urban sewage, slaughterhouse, and river water samples. PAdV and BPyV were detected in a very high percentage of samples potentially affected by either porcine or bovine fecal contamination, respectively. However, BAdV were detected in only one sample, showing a lower prevalence than BPyV in the wastewater samples analyzed. The 22 slaughterhouse samples with fecal contamination of animal origin showed negative results for the presence of HAdV. The river water samples analyzed were positive for the presence of both human and animal adenoviruses and polyomaviruses, indicating the existence of diverse sources of contamination. The identities of the viruses detected were confirmed by analyses of the amplified sequences. All BPyV isolates showed a 97% similarity in nucleotide sequences. This is the first time that PAdV5, BAdV6, and BPyV have been reported to occur in environmental samples. Human and porcine adenoviruses and human and bovine polyomaviruses are proposed as tools for evaluating the presence of viral contamination and for tracking the origin of fecal/urine contamination in environmental samples.

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Perfluorooctanoate and perfluorooctane sulfonate in South African river water

Water Science & Technology ◽

10.2166/wst.2013.566 ◽

2013 ◽

Vol 69 (1) ◽

pp. 185-194 ◽

Cited By ~ 24

Author(s):

J. B. N. Mudumbi ◽

S. K. O. Ntwampe ◽

F. M. Muganza ◽

J. O. Okonkwo

Keyword(s):

South Africa ◽

River Water ◽

Water Samples ◽

Suspended Solids ◽

Limit Of Detection ◽

Solid Phase ◽

Perfluorooctane Sulfonate ◽

Western Cape ◽

River Water Samples ◽

Salt River

This study examined the prevalence of perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) in river water samples (n = 56) and suspended solids (n = 5) from three major Western Cape rivers, in South Africa. Solid phase extraction (SPE) followed by liquid chromatography combined with electrospray tandem mass spectrometry (LC-MS/MS) using an analytical method developed in ISO 25101 (2009), PFOS and PFOA concentration in river water and in suspended solids from the rivers was investigated and quantified. From the results, PFOA and PFOS were detected in all the river water samples and were found in concentrations up to 314 and 182 ng/L for Diep River; 390 and 47 ng/L for Salt River; and 146 and 23 ng/L for Eerste River, respectively. In suspended solids, concentrations for PFOS and PFOA were 28 and 26 ng/g for Diep River; 16 and less than limit of detection for Eerste River; and 14 and 5 ng/g for Salt River, respectively. Some of these concentrations are higher than those previously reported in similar studies in various countries, and this suggests there is a cause for concern, in the Western Cape, South Africa, particularly in catchments where river and ground water is drawn for agricultural purposes in the province.

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Filtration extraction method using microfluidic channel for measuring environmental DNA

10.22541/au.163854179.99663512/v1 ◽

2021 ◽

Author(s):

Takashi Fukuzawa ◽

Yuichi Kameda ◽

Hisao Nagata ◽

Naofumi Nishizawa ◽

Hideyuki Doi

Keyword(s):

Water Sample ◽

River Water ◽

Dna Extraction ◽

Water Samples ◽

Extraction Method ◽

Microfluidic Channel ◽

Pcr Amplification ◽

Environmental Dna ◽

Laboratory Analysis ◽

River Water Samples

The environmental DNA (eDNA) method, which is widely applied for biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, Biryu-Chip (BC), and a filtration/extraction method, BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of the extracted DNA was obtained with 1/20–1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we could perform on-site measurements of eDNA within 30 min using a mobile PCR device. Using the BC method, filtration and extraction could be performed easily and quickly. The PCR results obtained by the BC method were similar to those obtained by the Sterivex method. The BC method required fewer steps and therefore, the risk of DNA contamination could be reduced. When combined with a mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from a few 10 mL of the water sample, even on-site.

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Filtration extraction method using microfluidic channel for measuring environmental DNA

10.1101/2021.11.18.468931 ◽

2021 ◽

Author(s):

Fukuzawa Takashi ◽

Yuichi Kameda ◽

Hisao Nagata ◽

Naofumi Nishizawa ◽

Hideyuki Doi

Keyword(s):

Water Sample ◽

River Water ◽

Dna Extraction ◽

Water Samples ◽

Extraction Method ◽

Microfluidic Channel ◽

Pcr Amplification ◽

Environmental Dna ◽

Laboratory Analysis ◽

River Water Samples

The environmental DNA (eDNA) method, which is widely applied for biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, Biryu-Chip (BC), and a filtration/extraction method, BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of the extracted DNA was obtained with 1/20-1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we could perform on-site measurements of eDNA within 30 min using a mobile PCR device. Using the BC method, filtration and extraction could be performed easily and quickly. The PCR results obtained by the BC method were similar to those obtained by the Sterivex method. However, the BC method required fewer steps and therefore, the risk of DNA contamination could be reduced. When combined with a mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from 10 mL of the water sample, even on-site.

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Ecotoxicological studies using modified ames bioassay

Water Science & Technology ◽

10.2166/wst.1996.0594 ◽

1996 ◽

Vol 34 (7-8) ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

M. Filipic ◽

M. J. Toman

Keyword(s):

River Water ◽

Water Samples ◽

Mutagenic Activity ◽

Municipal Waste ◽

Waste Dump ◽

River Water Samples ◽

Modified Method ◽

Mutagenicity Assay ◽

Wastewater Samples ◽

The Impact

Health and environmental risk assessment of river and wastewaters based on single chemicals is limited by the number of chemicals that can be identified and to those chemicals for which toxicity and mutagenicity data exist. In this study Salmonella/microsome mutagenicity assay was evaluated as a potentially useful biomonitoring system for river water and wastewater. Standard assay was modified to allow testing of up to 2.5 ml of nonconcentrated water sample and by introducing 90 minutes of preincubation. Mutagenic activity of nonconcentrated samples was compared to the mutagenic activity of XAD-2 extracts of the same samples. Eighteen river water samples, two wastewater samples and one sample of water leaking from municipal waste dump were tested. Mutagenicity was detected in three nonconcentrated river water samples, both nonconcentrated wastewater samples and in the sample of the water leaking from the municipal waste dump. The mutagenic profiles of nonconcentrated samples were different from the mutagenic profiles of the XAD-2 extracts. The modified method was sensitive enough to detect mutagens present in more polluted river water (class IV), in wastewaters and in water leaking from the municipal dump. For the assessment of the impact of the mutagenic river and wastewaters on the environment, calculations from the results of nonconcentrated samples should be used as it seems that calculations from the results of the extracts are leading to the underestimation of mutagenic potency. Mutagenic profiles of the extracts are a useful guide for further chemical and biological analysis to trace the sources of the mutagens and to introduce measures to reduce them.

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Application of membrane processes in fractionation of elements in river water

Water Science & Technology ◽

10.2166/wst.2015.444 ◽

2015 ◽

Vol 72 (12) ◽

pp. 2277-2290 ◽

Cited By ~ 1

Author(s):

N. Wu ◽

Y. Wyart ◽

J. Rose ◽

B. Angeletti ◽

P. Moulin

Keyword(s):

River Water ◽

Water Samples ◽

Membrane Filtration ◽

Water Mass ◽

Treatment Plant ◽

Industrial Area ◽

River Water Samples ◽

Anthropogenic Inputs ◽

Flux Decline ◽

Water Mass Balance

The influence of wastewater treatment plant (WWTP) effluents from one microelectronic industrial zone on element concentrations and partitioning in river water was investigated. The stepwise membrane filtration is used to distinguish different size fractions including large particulate (>18 μm), particulate (0.2–18 μm), colloidal/nanoparticle (10 kDa–0.2 μm) and truly dissolved fractions (<10 kDa) in river water samples and WWTP effluents. Results demonstrated that anthropogenic inputs (WWTP effluents and industrial area) had an important influence on concentrations and partitioning of some elements in river water. Mass balance results showed that membrane filtration processes could realize a good fractionation for many elements (good recoveries) in water samples. Flux decline during 0.2 μm and 10 kDa filtrations were analyzed, and corresponding fouling mechanisms are discussed.

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Faculty Opinions recommendation of Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1091365.545802 ◽

2007 ◽

Author(s):

Peter Williams

Keyword(s):

River Water ◽

Water Samples ◽

Conjugative Transfer ◽

River Water Samples ◽

Degradative Plasmid

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Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues

Metabolites ◽

10.3390/metabo11040240 ◽

2021 ◽

Vol 11 (4) ◽

pp. 240

Author(s):

Alison Woodward ◽

Alina Pandele ◽

Salah Abdelrazig ◽

Catherine A. Ortori ◽

Iqbal Khan ◽

...

Keyword(s):

Metabolic Pathways ◽

Extraction Method ◽

Limit Of Detection ◽

Rna Extraction ◽

Extraction Process ◽

Extraction Methods ◽

Serum Starvation ◽

Extraction Techniques ◽

Metabolic Genes ◽

Dual Extraction

The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.

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